diff shuffleBed.xml @ 17:44867b59dbf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174

--- a/shuffleBed.xml	Fri Aug 18 15:33:08 2017 -0400
+++ b/shuffleBed.xml	Tue Sep 05 15:40:14 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_shufflebed" name="ShuffleBed" version="@WRAPPER_VERSION@.1">
     <description>randomly redistrubute intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -8,7 +8,7 @@
     <command>
 <![CDATA[
         bedtools shuffle
-        -g '$genome'
+        -g @GENOME_FILE@
         -i '$inputA'
         $bedpe
         #if str($seed.seed_choose) == "True":
@@ -31,7 +31,7 @@
     <inputs>
         <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/>
         <param name="bedpe" type="boolean" label="The file is in BEDPE format" checked="False" truevalue="-bedpe" falsevalue="" />
-        <expand macro="genome" />
+        <expand macro="input_conditional_genome_file" />
         <param name="chrom" type="boolean" checked="False" truevalue="-chrom" falsevalue=""
             label="Keep features in the input file on the same chromosome"
             help="Solely permute their location on the chromosome. By default, both the chromosome and position are randomly chosen. (-chrom)" />
@@ -67,6 +67,7 @@
     <tests>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="shuffleBed.len" ftype="tabular" />
             <param name="chrom" value="" />
             <param name="seed_choose" value="True" />
@@ -75,6 +76,7 @@
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="shuffleBed.len" ftype="tabular" />
             <param name="chrom" value="True" />
             <param name="seed_choose" value="True" />
@@ -83,6 +85,7 @@
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="shuffleBed.len" ftype="tabular" />
             <param name="excl" value="shuffleBed2.bed" ftype="bed" />
             <param name="seed_choose" value="True" />
@@ -91,6 +94,7 @@
         </test>
         <test>
             <param name="inputA" value="shuffleBed1.bed" ftype="bed" />
+            <param name="genome_file_opts_selector" value="hist" />
             <param name="genome" value="shuffleBed.len" ftype="bed" />
             <param name="allow_beyond" value="True" />
             <param name="seed_choose" value="True" />